A new study from the University of Chicago published in Nature reveals that a Western-style diet rich in processed foods red meat dairy and sugar but low in fruits vegetables and whole grains significantly hinders the recovery of the gut microbiome after antibiotic use. Mice on this diet showed reduced microbial diversity and were more vulnerable to infections like Salmonella.

In contrast mice fed a diet resembling the Mediterranean style rich in plant-based fiber were able to quickly restore a healthy and resilient gut microbiome. We were really surprised by how dramatically different the recovery process is in the mice on the Western-style diet versus the healthier one said Megan Kennedy lead author and Medical Scientist Training Program student at UChicago.

Antibiotics can have a devastating effect on the gut microbiome. Though often given to treat infections by specific pathogens these drugs are indiscriminate. As a side effect they can wipe out entire communities of bacteria both the bad ones causing disease and the good commensal ones that help keep us healthy long-term.

Eugene B. Chang, the Martin Boyer Professor of Medicine at UChicago and a senior author on the study likens this to a forest fire suggesting natural rules of ecology apply when rebuilding the community of bacteria in the gut. 

The mammalian gut microbiome is like a forest and when you damage it, it must have a succession of events that occur in a specific order to restore itself back to its former health Chang said. When you are on a Western diet this does not happen because it doesn't provide the nutrients for the right microbes at the right time to recover.

They started with mice that were fed with food mimicking a typical modern diet or a mouse chow with diverse sources of plant fiber and low fat. Both groups were then treated with antibiotics. Later some mice continued the same diet while others were switched to the different diet.

The researchers also reintroduced microbes to the mice after antibiotics through fecal microbial transplants. The rationale behind using these transplants is that it can restore a healthy equilibrium in the gut by transferring microbes in the stool from one healthy animal to another. 

When the researchers analyzed the makeup of microbes in these different test groups they saw that only the mice on the plant fiber-rich diet either before or after antibiotics were able to recover to a healthy equilibrium of microbes. Further analysis by Christopher Henry a computational biologist at Argonne National Laboratory and his group showed that this diet promotes networks of metabolites that set the stage for microbes to rebuild a healthy ecosystem. 

In contrast fecal microbial transplants had a negligible impact on recovery among the mice on Western diets after antibiotics. These mice were also susceptible to infection with Salmonella a common intestinal pathogen.

Source: https://news.uchicago.edu/story/mice-diet-works-better-fecal-transplants-repair-gut-microbiome#:~:text=UChicago%20study%20shows%20microbiome%20struggles,a%20huge%20impact%20on%20health.